Technical Abstract:
Microarrays allow analysis of expression patterns of thousands of genes within the confines of one experiment. Arrays are direct descendants of DNA gel-blot (Southern) based assays that exploit interactions between complimentary strands of DNA. The addition of a solid glass substrate, precision robotics, and the use of fluorescence provide expression arrays with increased precision, speed, and scale over their filter and radioactivity based cousins. These qualities make microarrays a particularly attractive partner for the huge amounts of gene sequence information generated in the current genomics era. Although transcript monitoring is currently the most popular use for arrays, they have been successfully utilized in fields ranging from mutation detection to evolutionary sequence analysis. Microarray publications seem to appear with increasing fervor, however very few concern work in the plant sector. Here we provide a basic outline of microarray construction and use as we have optimized for our work with plant species (in particular tomato), with focus on sample preparation, probe synthesis, and data generation.